For gap penalty details you'd need to read the kent source. including files in these dirs: kent/src/ blat/ jkOwnLib/ lib/
Can you provide BLAT commandline and possibly query and target sample to reproduce the score behavior you saw? Please include psl output row(s) if you can. Generally people don't much bother with using BLAT's own commandline options for minScore, etc. They use pslReps and pslCDnaFilter utilities, or write their own filter, as suits their project or experiment. -Galt Ar 4/21/2010 12:48 PM, scríobh Peng Yu: > I'm wondering what "some sort of gap penalty" refers to. Also I query > 25bp sequence using the default, BLAT still gives the result. By > definition 25bp sequence should at most have a score of 25, which is > less than 30. Why the query still returns the the result? > > -minScore=N sets minimum score. This is the matches minus the > mismatches minus some sort of gap penalty. Default is 30 > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
